Secondary ion mass spectrometry (SIMS) is a well-established technique that permits rapid detection of stable and radioactive nuclides. Its resolving mass power provides an efficient analytical method and, in particular, it makes possible accurate isotopic ratio determination. Tests were carried out to evaluate the performance of this technique for the assessment of trace concentrations of uranium and plutonium in urine samples prepared in thin sources. Special attention has been paid to the preparation of the specimens which represents a critical step for the employment of this technique due to the erosion process used by SIMS. Fixation of the matrix in Polypyrrole films have been proved to be suitable. Present results show that concentrations in the order of 10–10 g·1–1 of238U (10–6 Bq·1–1) and 10–11 g·1–1 of239Pu (10–2 Bq·1–1) can be rapidly measured.